2.5. TRAJS#

2.5.1. MD Trajectories#

The TRAJS module performs the extraction of simulated trajectory from GROMACS program. It can be used from the command:

trajs ⟨simbox.gro⟩ [⟨-options⟩]

Note

Simply type trajs in the terminal and press enter to see the full list of execution options for the module.

2.5.2. Execution Options#

trajs ⟨trajectory.gro/xtc⟩ [⟨-options⟩]

  -------------------------------------------------------------------------------------------------
     auto : Execute an automated trajectory extraction from simulation files.                      [-ta](●)(■)
          » Description
            btrj = 1000 blocks with 10% extraction
          » NOTE: this option is recommended in queue systems.
          + #1: Individual Options - (no data analysis) ------------------------------
     -itr = I     : Extracts position structure #I from the trajectory.                            [-it](●)(■)⁽†⁾
     -ntr = N     : Extract N equaly spaced MD steps for truncated trajectory.                     [-nt](●)(■)
     -str = M     : Extract equaly spaced frames at every M steps from trajectory.                 [-st](●)(■)
          + #2: Combinable Options - (with data analysis) ----------------------------
     -ctr = [I:J] : Skip I equilibration steps and extract J production steps.                     [-ct](●)(■)⁽*⁾
     -btr = [B:X] : Select frames from B trajectory blocks into X% final steps.                    [-bt]   (■)⁽*⁾
     -ptr = [P:D] : Select configurations around pressure P with tolerance ±D (in bar).            [-pt]   (■)⁽*⁾
          + #3: Output file formats - (GROMACS only) ---------------------------------
     -xyz : Output in XYZ file format. [default]                                                   [-xy]   (■)
     -pdb : Output in PDB file format.                                                             [-pd]   (■)
     -gro : Output in GRO file format.                                                             [-gr]   (■)
          + #4: Other Options --------------------------------------------------------
     -prd : Select configuration production steps only and the corresponding properties.           [-pr](●)(■)⁽*⁾
     -grp : Extract short-ranged non-bonded potential energies.                                    [-gr]   (■)⁽*⁾
     -nbx : Don´t make corrections for “fragmented” molecules near the box edges.                  [-nb]   (■)
     -bak : Save intermediate PDB and XVG files for alternative convertions.                       [-bk]   (■)
     -deb : Save intermediate XVG file and create a reconstructed ENT file.                        [-db]   (■)
     -for : Force new extraction and override previous PDB file.                                   [-fm](●)(■)
  -------------------------------------------------------------------------------------------------
  ⁽*⁾ Configurable options in automated mode. (●) ORCA available. (■) GROMACS available.
  ⁽†⁾ Structure position, not configuration step.

2.5.3. Quickstart Examples#

  • Under construction…